[Plugin: WP Easy Post Types] deactivating plugin deletes custom post types?

I needed to test whether Easy Post Types was causing a conflict with another plugin, so deactivated it for a few minutes.

When I reactivated it, all the custom post types and fields I set up with the plugin were gone! Thankfully I had made a backup prior to deactivating it, but it still gave me quite a scare!

Doesn’t WP deactivate all plugins during the upgrade process? If so, then I’m likely to lose everything again when I upgrade.

Has anyone else experienced the same problem? Because if so, it seems like a pretty serious bug!